Calcium in PDB 4zmo: Crystal Structure of Human P-Cadherin (Ss-Dimer K14E)

The structure of Crystal Structure of Human P-Cadherin (Ss-Dimer K14E), PDB code: 4zmo was solved by J.M.M.Caaveiro, S.Kudo, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.43 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.380, 81.230, 48.990, 90.00, 105.79, 90.00
R / Rfree (%)	19.9 / 23.5

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-Dimer K14E) (pdb code 4zmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-Dimer K14E), PDB code: 4zmo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human P-Cadherin (Ss-Dimer K14E)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human P-Cadherin (Ss-Dimer K14E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:41.1 occ:1.00 OD2 A:ASP103 2.1 40.2 1.0 OD1 A:ASP100 2.2 43.3 1.0 OE2 A:GLU69 2.3 37.6 1.0 OE2 A:GLU11 2.4 40.0 1.0 O A:GLN101 2.4 43.5 1.0 OD1 A:ASP136 2.5 46.9 1.0 OE1 A:GLU69 2.8 40.7 1.0 CD A:GLU69 2.8 40.1 1.0 CG A:ASP136 3.2 39.6 1.0 CG A:ASP103 3.3 44.5 1.0 CG A:ASP100 3.3 44.2 1.0 CD A:GLU11 3.4 41.2 1.0 C A:GLN101 3.6 44.4 1.0 CB A:ASP136 3.7 35.6 1.0 OE1 A:GLU11 3.8 41.9 1.0 N A:ASP103 3.9 51.1 1.0 OD2 A:ASP100 3.9 42.2 1.0 OD1 A:ASP103 3.9 44.7 1.0 N A:GLN101 3.9 42.4 1.0 CA A:ASP136 3.9 37.9 1.0 OD2 A:ASP136 4.0 46.0 1.0 ND1 A:HIS104 4.2 51.4 1.0 CG A:GLU69 4.2 37.9 1.0 NE A:ARG68 4.4 42.1 1.0 CA A:GLN101 4.4 44.2 1.0 CB A:ASP103 4.5 42.5 1.0 CB A:ASP100 4.5 40.5 1.0 NH2 A:ARG68 4.5 43.6 1.0 N A:ASN102 4.5 47.9 1.0 CA A:ASP100 4.6 39.8 1.0 CA A:ASP103 4.6 46.7 1.0 CA A:ASN102 4.7 48.1 1.0 N A:ASP136 4.7 39.4 1.0 C A:ASP100 4.7 40.0 1.0 CG A:GLU11 4.7 41.2 1.0 C A:ASN102 4.8 47.3 1.0 CE1 A:HIS104 4.8 49.0 1.0 N A:HIS104 4.9 47.5 1.0 CB A:ARG68 5.0 34.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human P-Cadherin (Ss-Dimer K14E)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human P-Cadherin (Ss-Dimer K14E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:47.8 occ:1.00 O A:ASN143 2.1 37.0 1.0 O A:HIS104 2.2 45.7 1.0 OD1 A:ASN102 2.3 52.0 1.0 OD2 A:ASP134 2.3 48.6 1.0 OD1 A:ASP134 2.5 52.6 1.0 OD2 A:ASP136 2.5 46.0 1.0 OD2 A:ASP195 2.6 54.0 1.0 CG A:ASP134 2.7 49.6 1.0 C A:ASN143 3.4 44.7 1.0 C A:HIS104 3.4 51.3 1.0 CG A:ASP136 3.4 39.6 1.0 CG A:ASN102 3.4 52.9 1.0 CG A:ASP195 3.5 55.1 1.0 CB A:ASP195 3.7 53.0 1.0 CB A:ASP136 3.8 35.6 1.0 ND2 A:ASN102 4.1 57.6 1.0 CA A:HIS104 4.2 49.8 1.0 CB A:ASP134 4.2 46.8 1.0 N A:HIS104 4.2 47.5 1.0 CA A:ASN143 4.3 45.5 1.0 N A:GLY144 4.3 43.1 1.0 CB A:HIS104 4.4 49.6 1.0 N A:LYS105 4.4 54.8 1.0 OD1 A:ASP136 4.4 46.9 1.0 CA A:GLY144 4.5 44.9 1.0 CB A:ASN143 4.6 46.0 1.0 CA A:LYS105 4.6 57.8 1.0 CB A:ASN102 4.6 47.6 1.0 OD1 A:ASP195 4.7 59.7 1.0 CA A:ASN102 4.7 48.1 1.0 N A:ASP136 4.7 39.4 1.0 C A:LYS105 4.8 57.7 1.0 CA A:ASP136 4.9 37.9 1.0 C A:ASN102 4.9 47.3 1.0

S.Kudo, J.M.Caaveiro, K.Tsumoto. Adhesive Dimerization of Human P-Cadherin Catalyzed By A Chaperone-Like Mechanism Structure V. 24 1523 2016.
ISSN: ISSN 0969-2126
PubMed: 27545624
DOI: 10.1016/J.STR.2016.07.002